2024-07-16 alchemiscale : user group meeting notes

alchemiscale.org

• user questions, issues, requests

  • JS: Are we going to get non-eq-cycling on alchemiscale on soon?

  • DD: Yes, working on resolving feflow stuff so we can get a release cut, concern is on if we release too soon it could cause issues

  • JS: ETA?

  • DD: Should be days, better to make releases

  • JS: This PR adds the NEQ support in asapdiscovery

• compute resources status

• current stack versions:

  • python 3.10

  • alchemiscale: 0.4.0

  • neo4j: 5.18

  • gufe: 0.9.5

  • openfe: 0.14.0

    • DD: When we deploy 0.5.0, we will bump gufe and openfe to latest 1.x

  • perses: protocol-neqcyc

    • DD: This will be dropped in 0.5.0

  • openmmforcefields: 0.12.0

    • MH : working to re-add GAFF support to openmmforcefields; work happening here:

    • JW : can we make a new release of openmmforcefields (0.14.0) that only works with latest OpenMM, then release another that has MH’s patch that works with all OpenMM versions (0.15.0)?

    • MH : yes, I think that approach makes sense

    • MT: Will take responsibility for 0.14.0 release

      • JW : will want to pin to newest OpenMM 8.1.2 or newer in the conda-forge feedstock

DD: alchemiscale release 0.5.0 imminent; milestone complete

• includes:

  • openfe + gufe 1.0 compatibility

  • Folding@Home compute support

  • feflow inclusion, drop of perses

    • DD: What python version do people want?

    • MH: Grab the higest version of python that resolves the env given our other pins

• will be deployed on a new host, new database as api.alchemiscale.org with advance notice to users

  • current api.alchemiscale.org instance will be moved to api.legacy.alchemiscale.org, kept around for some time, but with no new compute provisioned

DD : will be working on testing MIG splitting on Lilac A100 after alchemiscale 0.5.0 deployed to alchemiscale.org

IA : feflow and settings changes that are backwards-incompatible

• DD: We are meeting tomorow to talk about these changes

MT : all packages will soon be on pydantic v2

• MT: Example of how v1 & v2 APIs CANNOT mix: Best way to serialize an Interchange to JSON? · openforcefield openff-bespokefit · Discussion #328

• DD: PR working on it , tests pass locally but on CI it just hangs and times out after 6 hours

• JW: The PR is nice since it migrates to native v2, but you can install pydantic 2 and use the v1 api, which works fine as long as you don’t mix them

• MT: The PR to using the v1 api when installing the pydantic 2 pacakge is an easy PR, mostly copy and paste different imports